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Obsolete five OBA terms with obsoleted PRO entities
Co-authored-by: ar-ibrahim <97462656+ar-ibrahim@users.noreply.github.com>
1 parent 9336d1e commit ab8ca71

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Lines changed: 40 additions & 63 deletions

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‎src/ontology/components/obsoletes.owl‎

Lines changed: 32 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
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Ontology(<http://purl.obolibrary.org/obo/oba/components/obsoletes.owl>
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<http://purl.obolibrary.org/obo/oba/releases/2025-07-08/components/obsoletes.owl>
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Annotation(owl:versionInfo "2025-07-08")
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<http://purl.obolibrary.org/obo/oba/releases/2025-10-29/components/obsoletes.owl>
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Annotation(owl:versionInfo "2025-10-29")
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000037>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000039>))
@@ -77,7 +77,12 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001041>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001042>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001043>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001044>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2043233>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2044443>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050081>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2058599>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2059278>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2081815>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0000187>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0002918>))
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Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0003952>))
@@ -426,12 +431,37 @@ AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_1001043>
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/OBA_1001044> <http://purl.obolibrary.org/obo/OBA_VT0007031>)
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_1001044> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/OBA_2043233> (<http://purl.obolibrary.org/obo/OBA_2043233>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2043233> "Reason for obsoletion: The protein entity PR:000013872 (regenerating islet-derived protein 3-gamma) has been obsoleted by the Protein Ontology.")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2043233> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/OBA_2044443> (<http://purl.obolibrary.org/obo/OBA_2044443>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2044443> "Reason for obsoletion: The protein entity PR:000030596 (putative uncharacterized protein TXNRD3NB) has been obsoleted by the Protein Ontology.")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2044443> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/OBA_2050081> (<http://purl.obolibrary.org/obo/OBA_2050081>)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/OBA_2050081> <http://purl.obolibrary.org/obo/OBA_2045319>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2050081> "Reason for obsoletion: a term with the same intended meaning already exists.")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2050081> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/OBA_2058599> (<http://purl.obolibrary.org/obo/OBA_2058599>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2058599> "Reason for obsoletion: The protein entity PR:Q12799 (putative T-complex protein 10A homolog (human)) has been obsoleted by the Protein Ontology.")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2058599> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/OBA_2059278> (<http://purl.obolibrary.org/obo/OBA_2059278>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2059278> "Reason for obsoletion: The protein entity PR:Q6F5E7 (putative uncharacterized protein TXNRD3NB (human)) has been obsoleted by the Protein Ontology.")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2059278> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/OBA_2081815> (<http://purl.obolibrary.org/obo/OBA_2081815>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2081815> "Reason for obsoletion: The protein entity PR:Q9Y4X1 (UDP-glucuronosyltransferase 2A1 (human)) has been obsoleted by the Protein Ontology.")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2081815> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/OBA_VT0000187> (<http://purl.obolibrary.org/obo/OBA_VT0000187>)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/OBA_VT0000187> <http://purl.obolibrary.org/obo/OBA_2040183>)

‎src/patterns/data/default/entity_attribute_location.tsv‎

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -3314,7 +3314,6 @@ OBA:2043229 level of receptor expression-enhancing protein 2 in blood serum PR:0
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OBA:2043230 level of lithostathine-1-alpha in blood serum PR:000013869 lithostathine-1-alpha PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2043231 level of lithostathine-1-beta in blood serum PR:000013870 lithostathine-1-beta PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
33163316
OBA:2043232 level of regenerating islet-derived protein 3-alpha in blood serum PR:000013871 regenerating islet-derived protein 3-alpha PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2043233 level of regenerating islet-derived protein 3-gamma in blood serum PR:000013872 regenerating islet-derived protein 3-gamma PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2043234 level of transcription factor RelB in blood serum PR:000013876 transcription factor RelB PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2043235 level of RELT-like protein 1 in blood serum PR:000013877 RELT-like protein 1 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
33203319
OBA:2043236 level of RELT-like protein 2 in blood serum PR:000013878 RELT-like protein 2 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
@@ -4524,7 +4523,6 @@ OBA:2044439 level of protein FAM171A1 in blood serum PR:000030586 protein FAM171
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OBA:2044440 level of V-set and immunoglobulin domain-containing protein 8 in blood serum PR:000030592 V-set and immunoglobulin domain-containing protein 8 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2044441 level of protein FAM162B in blood serum PR:000030593 protein FAM162B PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2044442 level of metallophosphoesterase MPPED2 in blood serum PR:000030594 metallophosphoesterase MPPED2 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2044443 level of putative uncharacterized protein TXNRD3NB in blood serum PR:000030596 putative uncharacterized protein TXNRD3NB PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2044444 level of E3 ubiquitin-protein ligase HECTD3 in blood serum PR:000030605 E3 ubiquitin-protein ligase HECTD3 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2044445 level of transmembrane protein 185A in blood serum PR:000030611 transmembrane protein 185A PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
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OBA:2044446 level of piezo-type mechanosensitive ion channel component 1 in blood serum PR:000030614 piezo-type mechanosensitive ion channel component 1 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
@@ -11013,7 +11011,6 @@ OBA:2058595 level of twinfilin-1 (human) in cerebrospinal fluid PR:Q12792 twinfi
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OBA:2058596 level of hyaluronidase-1 (human) in cerebrospinal fluid PR:Q12794 hyaluronidase-1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2058597 level of aspartyl/asparaginyl beta-hydroxylase (human) in cerebrospinal fluid PR:Q12797 aspartyl/asparaginyl beta-hydroxylase (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2058598 level of centrin-1 (human) in cerebrospinal fluid PR:Q12798 centrin-1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2058599 level of obsolete putative T-complex protein 10A homolog (human) in cerebrospinal fluid PR:Q12799 obsolete putative T-complex protein 10A homolog (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
1101711014
OBA:2058600 level of EGF-containing fibulin-like extracellular matrix protein 1 (human) in cerebrospinal fluid PR:Q12805 EGF-containing fibulin-like extracellular matrix protein 1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
1101811015
OBA:2058601 level of nucleosome-remodeling factor subunit BPTF (human) in cerebrospinal fluid PR:Q12830 nucleosome-remodeling factor subunit BPTF (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
1101911016
OBA:2058602 level of zona pellucida sperm-binding protein 4 (human) in cerebrospinal fluid PR:Q12836 zona pellucida sperm-binding protein 4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
@@ -11692,7 +11689,6 @@ OBA:2059274 level of interleukin-31 (human) in cerebrospinal fluid PR:Q6EBC2 int
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OBA:2059275 level of small ubiquitin-related modifier 4 (human) in cerebrospinal fluid PR:Q6EEV6 small ubiquitin-related modifier 4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2059276 level of C-type lectin domain family 6 member A (human) in cerebrospinal fluid PR:Q6EIG7 C-type lectin domain family 6 member A (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2059277 level of vasorin (human) in cerebrospinal fluid PR:Q6EMK4 vasorin (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2059278 level of obsolete putative uncharacterized protein TXNRD3NB (human) in cerebrospinal fluid PR:Q6F5E7 obsolete putative uncharacterized protein TXNRD3NB (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2059279 level of secreted frizzled-related protein 4 (human) in cerebrospinal fluid PR:Q6FHJ7 secreted frizzled-related protein 4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2059280 level of fatty-acid amide hydrolase 2 (human) in cerebrospinal fluid PR:Q6GMR7 fatty-acid amide hydrolase 2 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
1169811694
OBA:2059281 level of putative peptidyl-tRNA hydrolase PTRHD1 (human) in cerebrospinal fluid PR:Q6GMV3 putative peptidyl-tRNA hydrolase PTRHD1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
@@ -14229,7 +14225,6 @@ OBA:2081811 level of cysteine protease ATG4B (human) in cerebrospinal fluid PR:Q
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OBA:2081812 level of transducin beta-like protein 2 (human) in cerebrospinal fluid PR:Q9Y4P3 transducin beta-like protein 2 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2081813 level of sperm flagellar protein 1 (human) in cerebrospinal fluid PR:Q9Y4P9 sperm flagellar protein 1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2081814 level of cyanocobalamin reductase / alkylcobalamin dealkylase (human) in cerebrospinal fluid PR:Q9Y4U1 cyanocobalamin reductase / alkylcobalamin dealkylase (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2081815 level of obsolete UDP-glucuronosyltransferase 2A1 (human) in cerebrospinal fluid PR:Q9Y4X1 obsolete UDP-glucuronosyltransferase 2A1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
1423314228
OBA:2081816 level of C-C motif chemokine 27 (human) in cerebrospinal fluid PR:Q9Y4X3 C-C motif chemokine 27 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2081817 level of U6 snRNA-associated Sm-like protein LSm4 (human) in cerebrospinal fluid PR:Q9Y4Z0 U6 snRNA-associated Sm-like protein LSm4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
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OBA:2081818 level of neurogenin-3 (human) in cerebrospinal fluid PR:Q9Y4Z2 neurogenin-3 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744

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